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Annual Review of Plant Biology 2005Plastids are metabolically extraordinarily active and versatile organelles that are found in all plant cells with the exception of angiosperm pollen grains. Many of the... (Review)
Review
Plastids are metabolically extraordinarily active and versatile organelles that are found in all plant cells with the exception of angiosperm pollen grains. Many of the plastid-localized biochemical pathways depend on precursors from the cytosol and, in turn, many cytosolic pathways depend on the supply of precursor molecules from the plastid stroma. Hence, a massive traffic of metabolites occurs across the permeability barrier between plastids and cytosol that is called the plastid envelope membrane. Many of the known plastid envelope solute transporters have been identified by biochemical purification and peptide sequencing. This approach is of limited use for less abundant proteins and for proteins of plastid subtypes that are difficult to isolate in preparative amounts. Hence, the majority of plastid envelope membrane transporters are not yet identified at the molecular level. The availability of fully sequenced plant genomes, the progress in bioinformatics to predict membrane transporters localized in plastids, and the development of highly sensitive proteomics techniques open new avenues toward identifying additional, to date unknown, plastid envelope membrane transporters.
Topics: Amino Acid Sequence; Computational Biology; Genes, Plant; Intracellular Membranes; Membrane Transport Proteins; Molecular Sequence Data; Plants; Plastids; Sequence Homology, Amino Acid
PubMed: 15862092
DOI: 10.1146/annurev.arplant.56.032604.144228 -
Methods in Molecular Biology (Clifton,... 2021Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living...
Chloroplasts, the sites of photosynthesis and sources of reducing power, are at the core of the success story that sets apart autotrophic plants from most other living organisms. Along with their fellow organelles (e.g., amylo-, chromo-, etio-, and leucoplasts), they form a group of intracellular biosynthetic machines collectively known as plastids. These plant cell constituents have their own genome (plastome), their own (70S) ribosomes, and complete enzymatic equipment covering the full range from DNA replication via transcription and RNA processive modification to translation. Plastid RNA synthesis (gene transcription) involves the collaborative activity of two distinct types of RNA polymerases that differ in their phylogenetic origin as well as their architecture and mode of function. The existence of multiple plastid RNA polymerases is reflected by distinctive sets of regulatory DNA elements and protein factors. This complexity of the plastid transcription apparatus thus provides ample room for regulatory effects at many levels within and beyond transcription. Research in this field offers insight into the various ways in which plastid genes, both singly and groupwise, can be regulated according to the needs of the entire cell. Furthermore, it opens up strategies that allow to alter these processes in order to optimize the expression of desired gene products.
Topics: DNA-Binding Proteins; DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Plant Proteins; Plastids; Promoter Regions, Genetic; Transcription, Genetic
PubMed: 34028762
DOI: 10.1007/978-1-0716-1472-3_2 -
International Review of Cytology 2005Plastids are semiautonomous plant organelles exhibiting their own transcription-translation systems that originated from a cyanobacteria-related endosymbiotic... (Review)
Review
Plastids are semiautonomous plant organelles exhibiting their own transcription-translation systems that originated from a cyanobacteria-related endosymbiotic prokaryote. As a consequence of massive gene transfer to nuclei and gene disappearance during evolution, the extant plastid genome is a small circular DNA encoding only ca. 120 genes (less than 5% of cyanobacterial genes). Therefore, it was assumed that plastids have a simple transcription-regulatory system. Later, however, it was revealed that plastid transcription is a multistep gene regulation system and plays a crucial role in developmental and environmental regulation of plastid gene expression. Recent molecular and genetic approaches have identified several new players involved in transcriptional regulation in plastids, such as multiple RNA polymerases, plastid sigma factors, transcription regulators, nucleoid proteins, and various signaling factors. They have provided novel insights into the molecular basis of plastid transcription in higher plants. This review summarizes state-of-the-art knowledge of molecular mechanisms that regulate plastid transcription in higher plants.
Topics: DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Phylogeny; Plant Structures; Plastids; Promoter Regions, Genetic; Transcription Factors; Transcription, Genetic
PubMed: 16157177
DOI: 10.1016/S0074-7696(05)44001-2 -
Philosophical Transactions of the Royal... Jun 2020Plastid genes in higher plants are transcribed by at least two different RNA polymerases, the plastid-encoded RNA polymerase (PEP), a bacteria-like core enzyme whose... (Review)
Review
The plastid transcription machinery and its coordination with the expression of nuclear genome: Plastid-Encoded Polymerase, Nuclear-Encoded Polymerase and the Genomes Uncoupled 1-mediated retrograde communication.
Plastid genes in higher plants are transcribed by at least two different RNA polymerases, the plastid-encoded RNA polymerase (PEP), a bacteria-like core enzyme whose subunits are encoded by plastid genes (, , and ), and the nuclear-encoded plastid RNA polymerase (NEP), a monomeric bacteriophage-type RNA polymerase. Both PEP and NEP enzymes are active in non-green plastids and in chloroplasts at all developmental stages. Their transcriptional activity is affected by endogenous and exogenous factors and requires a strict coordination within the plastid and with the nuclear gene expression machinery. This review focuses on the different molecular mechanisms underlying chloroplast transcription regulation and its coordination with the photosynthesis-associated nuclear genes () expression. Particular attention is given to the link between NEP and PEP activity and the GUN1- (Genomes Uncoupled 1) mediated chloroplast-to-nucleus retrograde communication with respect to the adaptive response, i.e. the increased accumulation of NEP-dependent transcripts upon depletion of PEP activity, and the editing-level changes observed in NEP-dependent transcripts, including and , in cotyledons after norflurazon or lincomycin treatment. The role of cytosolic preproteins and HSP90 chaperone as components of the GUN1-retrograde signalling pathway, when chloroplast biogenesis is inhibited in cotyledons, is also discussed. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.
Topics: Cell Nucleus; Chloroplasts; DNA-Directed RNA Polymerases; Gene Expression Regulation, Plant; Genome, Plant; Photosynthesis; Plant Proteins; Plants; Plastids; Signal Transduction; Transcription, Genetic
PubMed: 32362266
DOI: 10.1098/rstb.2019.0399 -
Microbiological Research Feb 2021The unicellular, free-living, nonphotosynthetic chlorophycean alga Polytomella parva, closely related to Chlamydomonas reinhardtii and Volvox carteri, contains...
The unicellular, free-living, nonphotosynthetic chlorophycean alga Polytomella parva, closely related to Chlamydomonas reinhardtii and Volvox carteri, contains colorless, starch-storing plastids. The P. parva plastids lack all light-dependent processes but maintain crucial metabolic pathways. The colorless alga also lacks a plastid genome, meaning no transcription or translation should occur inside the organelle. Here, using an algal fraction enriched in plastids as well as publicly available transcriptome data, we provide a morphological and proteomic characterization of the P. parva plastid, ultimately identifying several plastid proteins, both by mass spectrometry and bioinformatic analyses. Data are available via ProteomeXchange with identifier PXD022051. Altogether these results led us to propose a plastid proteome for P. parva, i.e., a set of proteins that participate in carbohydrate metabolism; in the synthesis and degradation of starch, amino acids and lipids; in the biosynthesis of terpenoids and tetrapyrroles; in solute transport and protein translocation; and in redox homeostasis. This is the first detailed plastid proteome from a unicellular, free-living colorless alga.
Topics: Amino Acids; Chlorophyta; Genome, Plastid; Mass Spectrometry; Plastids; Proteome; Proteomics
PubMed: 33285428
DOI: 10.1016/j.micres.2020.126649 -
Tree Physiology Nov 2022The process of plastids developing into chloroplasts is critical for plants to survive. However, this process in woody plants is less understood. Kandelia obovata Sheue,...
The process of plastids developing into chloroplasts is critical for plants to survive. However, this process in woody plants is less understood. Kandelia obovata Sheue, Liu & Yong is a viviparous mangrove species; the seeds germinate on the maternal tree, and the hypocotyls continue to develop into mature propagules. We identified rare albino propagules through field observation among normal green and brown ones. Toward unveiling the propagule plastid development mechanism, albino propagule leaves only have etioplasts, low photosynthesis rates, and drastically reduced chlorophyll a/b and carotenoid contents, but with increased superoxide dismutase activities. To identify candidate genes controlling propagule plastid development, a genome-wide association study (GWAS) was performed between the albino and green propagules. Twenty-five significant single nucleotide polymorphisms (SNPs) were associated with albino propagule plastid development, the most significant SNPs being located on chromosomes 1 and 5. Significant differentially expressed genes were identified in porphyrin and chlorophyll metabolisms, carotenoid and flavonoid biosynthesis by combining transcriptome and GWAS data. In particular, KoDELLAs, encoding a transcription factor and KoCHS, encoding chalcone synthase, may be essential to regulate the albino propagules plastid development through weakened chlorophyll and flavonoid biosynthesis pathways while promoting chlorophyll degradation. Our results provide insights into genetic mechanisms regulating propagule plastid development in woody plants.
Topics: Rhizophoraceae; Genome-Wide Association Study; Chlorophyll A; Chlorophyll; Plastids; Carotenoids; Flavonoids
PubMed: 35708522
DOI: 10.1093/treephys/tpac063 -
Essays in Biochemistry Apr 2018Plastids are critical organelles in plant cells that perform diverse functions and are central to many metabolic pathways. Beyond their major roles in primary... (Review)
Review
Plastids are critical organelles in plant cells that perform diverse functions and are central to many metabolic pathways. Beyond their major roles in primary metabolism, of which their role in photosynthesis is perhaps best known, plastids contribute to the biosynthesis of phytohormones and other secondary metabolites, store critical biomolecules, and sense a range of environmental stresses. Accordingly, plastid-derived signals coordinate a host of physiological and developmental processes, often by emitting signalling molecules that regulate the expression of nuclear genes. Several excellent recent reviews have provided broad perspectives on plastid signalling pathways. In this review, we will highlight recent advances in our understanding of chloroplast signalling pathways. Our discussion focuses on new discoveries illuminating how chloroplasts determine life and death decisions in cells and on studies elucidating tetrapyrrole biosynthesis signal transduction networks. We will also examine the role of a plastid RNA helicase, ISE2, in chloroplast signalling, and scrutinize intriguing results investigating the potential role of stromules in conducting signals from the chloroplast to other cellular locations.
Topics: Chloroplasts; Genome, Plant; Oxidative Stress; Plants; Plastids; RNA Helicases; Signal Transduction; Tetrapyrroles
PubMed: 29563221
DOI: 10.1042/EBC20170011 -
Biotechnology Advances 2012In the past decades, the progress made in plant biotechnology has made possible the use of plants as a novel production platform for a wide range of molecules. In this... (Review)
Review
In the past decades, the progress made in plant biotechnology has made possible the use of plants as a novel production platform for a wide range of molecules. In this context, the transformation of the plastid genome has given a huge boost to prove that plants are a promising system to produce recombinant proteins. In this review, we provide a background on plastid genetics and on the principles of this technology in higher plants. Further, we discuss the most recent biotechnological applications of plastid transformation for the production of enzymes, therapeutic proteins, antibiotics, and proteins with immunological properties. We also discuss the potential of plastid biotechnology and the novel tools developed to overcome some limitations of chloroplast transformation.
Topics: Biotechnology; Chloroplasts; Plants, Genetically Modified; Plastids; Recombinant Proteins; Transformation, Genetic
PubMed: 21843626
DOI: 10.1016/j.biotechadv.2011.07.019 -
Trends in Plant Science Dec 2012Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of... (Review)
Review
Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.
Topics: Gene Expression Regulation, Plant; Plastids; RNA, Untranslated; Transcription Factors
PubMed: 22981395
DOI: 10.1016/j.tplants.2012.08.002 -
Trends in Genetics : TIG Apr 2009The concept of plastid signalling posits that signals originating from chloroplasts modulate nuclear gene expression (NGE). Put simply, it claims that signalling factors... (Review)
Review
The concept of plastid signalling posits that signals originating from chloroplasts modulate nuclear gene expression (NGE). Put simply, it claims that signalling factors are exported from the chloroplast, traverse the cytosol, and act in the nucleus. Pertinent signals are thought to derive from various sources, including the tetrapyrrole pathway, protein synthesis, reactive oxygen species, or the redox state of the organelle. Recent studies have cast doubt on the most popular candidate signalling molecule, the tetrapyrrole pathway intermediate Mg-protoporphyrin IX, indicating that chloroplast activity might control NGE indirectly by affecting cytosolic metabolite levels or redox states (metabolic signalling). Here, we focus on recent developments and confusions in the field of plastid signalling research and highlight alternative scenarios of plastid-nucleus signal transduction. Future analyses of chloroplast-nucleus communication should focus on providing an integrated view of plastid signalling under physiologically relevant conditions.
Topics: Animals; Cell Nucleus; Chlamydomonas reinhardtii; Chloroplasts; Models, Biological; Models, Genetic; Mutation; Oxidation-Reduction; Photosynthesis; Plastids; Reactive Oxygen Species; Signal Transduction; Tetrapyrroles
PubMed: 19303165
DOI: 10.1016/j.tig.2009.02.004